tests/testthat/test_natural_abundance_correction.R

In XiaoyangSu/AccuCor: Natural Abundance Correction of Mass Spectrometer Data

context("Natural abundance correction")
library(accucor)

read_expected <- function(file, sheet) {
  expected <- readxl::read_excel(path = file, sheet = sheet)
  expected <- dplyr::mutate_at(
    expected,
    dplyr::vars(dplyr::ends_with("_Label")),
    as.integer
  )
}

test_that("Carbon correction (Excel, simple format)", {
  resolution <- 100000
  input_file <- system.file(
    "extdata",
    "C_Sample_Input_Simple.xlsx",
    package = "accucor"
  )

  corrected <- natural_abundance_correction(
    path = input_file,
    output_base = FALSE,
    resolution = resolution
  )

  expected_output <- list(
    "Original" = read_expected(
      system.file(
        "extdata",
        "C_Sample_Input_Simple.xlsx",
        package = "accucor"
      ),
      sheet = 1
    ),
    "Corrected" = read_expected(
      system.file(
        "extdata",
        "C_Sample_Input_Simple_corrected.xlsx",
        package = "accucor"
      ),
      sheet = "Corrected"
    ),
    "Normalized" = read_expected(
      system.file(
        "extdata",
        "C_Sample_Input_Simple_corrected.xlsx",
        package = "accucor"
      ),
      sheet = "Normalized"
    ),
    "PoolAfterDF" = read_expected(
      system.file(
        "extdata",
        "C_Sample_Input_Simple_corrected.xlsx",
        package = "accucor"
      ),
      sheet = "PoolAfterDF"
    )
  )

  expect_equal(corrected, expected_output)
})


test_that("PoolBeforeDF parameter", {
  resolution <- 100000
  input_file <- system.file(
    "extdata",
    "C_Sample_Input_Simple.xlsx",
    package = "accucor"
  )

  corrected <- natural_abundance_correction(
    path = input_file,
    output_base = FALSE,
    report_pool_size_before_df = TRUE,
    resolution = resolution
  )

  expected_output <- list(
    "Original" = read_expected(
      system.file(
        "extdata",
        "C_Sample_Input_Simple.xlsx",
        package = "accucor"
      ),
      sheet = 1
    ),
    "Corrected" = read_expected(
      system.file(
        "extdata",
        "C_Sample_Input_Simple_corrected.xlsx",
        package = "accucor"
      ),
      sheet = "Corrected"
    ),
    "Normalized" = read_expected(
      system.file(
        "extdata",
        "C_Sample_Input_Simple_corrected.xlsx",
        package = "accucor"
      ),
      sheet = "Normalized"
    ),
    "PoolAfterDF" = read_expected(
      system.file(
        "extdata",
        "C_Sample_Input_Simple_corrected.xlsx",
        package = "accucor"
      ),
      sheet = "PoolAfterDF"
    ),
    "PoolBeforeDF" = read_expected(
      system.file(
        "extdata",
        "C_Sample_Input_Simple_corrected.xlsx",
        package = "accucor"
      ),
      sheet = "PoolBeforeDF"
    )
  )

  expect_equal(corrected, expected_output)
})

test_that("Carbon correction (csv, simple format)", {
  resolution <- 100000
  resolution_defined_at <- 200
  input_file <- system.file(
    "extdata",
    "C_Sample_Input_Simple.csv",
    package = "accucor"
  )

  corrected <- natural_abundance_correction(
    path = input_file,
    output_base = FALSE,
    resolution = resolution,
    resolution_defined_at = resolution_defined_at
  )

  expected_output <- list(
    "Original" = read_expected(
      system.file(
        "extdata",
        "C_Sample_Input_Simple.xlsx",
        package = "accucor"
      ),
      sheet = 1
    ),
    "Corrected" = read_expected(
      system.file(
        "extdata",
        "C_Sample_Input_Simple_corrected.xlsx",
        package = "accucor"
      ),
      sheet = "Corrected"
    ),
    "Normalized" = read_expected(
      system.file(
        "extdata",
        "C_Sample_Input_Simple_corrected.xlsx",
        package = "accucor"
      ),
      sheet = "Normalized"
    ),
    "PoolAfterDF" = read_expected(
      system.file(
        "extdata",
        "C_Sample_Input_Simple_corrected.xlsx",
        package = "accucor"
      ),
      sheet = "PoolAfterDF"
    )
  )

  expect_equal(corrected, expected_output)
})


test_that("Carbon correction (Excel, Classic MAVEN copy/paste)", {
  resolution <- 100000
  resolution_defined_at <- 200
  input_file <- system.file("extdata", "C_Sample_Input.xlsx",
    package = "accucor"
  )
  knowns_file <- system.file("extdata", "KNOWNS.csv", package = "accucor")
  corrected <- natural_abundance_correction(
    path = input_file,
    compound_database = knowns_file,
    output_base = FALSE,
    resolution = resolution,
    resolution_defined_at = resolution_defined_at
  )

  expected_output <- list(
    "Original" = read_expected(
      system.file(
        "extdata",
        "C_Sample_Input_Simple_corrected.xlsx",
        package = "accucor"
      ),
      sheet = 1
    ),
    "Corrected" = read_expected(
      system.file(
        "extdata",
        "C_Sample_Input_Simple_corrected.xlsx",
        package = "accucor"
      ),
      sheet = "Corrected"
    ),
    "Normalized" = read_expected(
      system.file(
        "extdata",
        "C_Sample_Input_Simple_corrected.xlsx",
        package = "accucor"
      ),
      sheet = "Normalized"
    ),
    "PoolAfterDF" = read_expected(
      system.file(
        "extdata",
        "C_Sample_Input_Simple_corrected.xlsx",
        package = "accucor"
      ),
      sheet = "PoolAfterDF"
    )
  )

  expect_equal(corrected, expected_output)
})


test_that("Deuterium correction (Excel, simple format)", {
  resolution <- 100000
  resolution_defined_at <- 200
  input_file <- system.file("extdata", "D_Sample_Input_Simple.xlsx",
    package = "accucor"
  )

  corrected <- natural_abundance_correction(
    path = input_file,
    output_base = FALSE,
    resolution = resolution,
    resolution_defined_at = resolution_defined_at
  )

  expected_output <- list(
    "Original" = read_expected(
      system.file(
        "extdata",
        "D_Sample_Input_Simple.xlsx",
        package = "accucor"
      ),
      sheet = 1
    ),
    "Corrected" = read_expected(
      system.file(
        "extdata",
        "D_Sample_Input_Simple_corrected.xlsx",
        package = "accucor"
      ),
      sheet = "Corrected"
    ),
    "Normalized" = read_expected(
      system.file(
        "extdata",
        "D_Sample_Input_Simple_corrected.xlsx",
        package = "accucor"
      ),
      sheet = "Normalized"
    ),
    "PoolAfterDF" = read_expected(
      system.file(
        "extdata",
        "D_Sample_Input_Simple_corrected.xlsx",
        package = "accucor"
      ),
      sheet = "PoolAfterDF"
    )
  )

  expect_equal(corrected, expected_output)
})


test_that("Deuterium correction (Excel, Classic Maven Cut/Paste)", {
  resolution <- 100000
  resolution_defined_at <- 200
  input_file <- system.file("extdata", "D_Sample_Input.xlsx",
    package = "accucor"
  )
  knowns_file <- system.file("extdata", "KNOWNS.csv", package = "accucor")

  corrected <- natural_abundance_correction(
    path = input_file,
    compound_database = knowns_file,
    output_base = FALSE,
    resolution = resolution, resolution_defined_at = resolution_defined_at
  )

  expected_output <- list(
    "Original" = read_expected(
      system.file(
        "extdata",
        "D_Sample_Input_Simple.xlsx",
        package = "accucor"
      ),
      sheet = 1
    ),
    "Corrected" = read_expected(
      system.file(
        "extdata",
        "D_Sample_Input_Simple_corrected.xlsx",
        package = "accucor"
      ),
      sheet = "Corrected"
    ),
    "Normalized" = read_expected(
      system.file(
        "extdata",
        "D_Sample_Input_Simple_corrected.xlsx",
        package = "accucor"
      ),
      sheet = "Normalized"
    ),
    "PoolAfterDF" = read_expected(
      system.file(
        "extdata",
        "D_Sample_Input_Simple_corrected.xlsx",
        package = "accucor"
      ),
      sheet = "PoolAfterDF"
    )
  )

  expect_equal(corrected, expected_output)
})


test_that("Nitrogen correction (Excel, simple format)", {
  resolution <- 140000
  resolution_defined_at <- 200
  input_file <- system.file(
    "extdata",
    "N_Sample_Input_Simple.xlsx",
    package = "accucor"
  )

  corrected <- natural_abundance_correction(
    path = input_file,
    output_base = FALSE,
    resolution = resolution,
    resolution_defined_at = resolution_defined_at
  )

  expected_output <- list(
    "Original" = read_expected(
      system.file(
        "extdata",
        "N_Sample_Input_Simple.xlsx",
        package = "accucor"
      ),
      sheet = 1
    ),
    "Corrected" = read_expected(
      system.file(
        "extdata",
        "N_Sample_Input_Simple_corrected.xlsx",
        package = "accucor"
      ),
      sheet = "Corrected"
    ),
    "Normalized" = read_expected(
      system.file(
        "extdata",
        "N_Sample_Input_Simple_corrected.xlsx",
        package = "accucor"
      ),
      sheet = "Normalized"
    ),
    "PoolAfterDF" = read_expected(
      system.file(
        "extdata",
        "N_Sample_Input_Simple_corrected.xlsx",
        package = "accucor"
      ),
      sheet = "PoolAfterDF"
    )
  )

  expect_equal(corrected, expected_output)
})


test_that("Nitrogen correction (Excel, Classic Maven Cut/Paste)", {
  resolution <- 140000
  resolution_defined_at <- 200
  input_file <- system.file(
    "extdata",
    "N_Sample_Input.xlsx",
    package = "accucor"
  )
  knowns_file <- system.file("extdata", "KNOWNS.csv", package = "accucor")

  corrected <- natural_abundance_correction(
    path = input_file,
    compound_database = knowns_file,
    output_base = FALSE,
    resolution = resolution,
    resolution_defined_at = resolution_defined_at
  )

  expected_output <- list(
    "Original" = read_expected(
      system.file(
        "extdata",
        "N_Sample_Input_Simple.xlsx",
        package = "accucor"
      ),
      sheet = 1
    ),
    "Corrected" = read_expected(
      system.file(
        "extdata",
        "N_Sample_Input_Simple_corrected.xlsx",
        package = "accucor"
      ),
      sheet = "Corrected"
    ),
    "Normalized" = read_expected(
      system.file(
        "extdata",
        "N_Sample_Input_Simple_corrected.xlsx",
        package = "accucor"
      ),
      sheet = "Normalized"
    ),
    "PoolAfterDF" = read_expected(
      system.file(
        "extdata",
        "N_Sample_Input_Simple_corrected.xlsx",
        package = "accucor"
      ),
      sheet = "PoolAfterDF"
    )
  )

  expect_equal(corrected, expected_output)
})


test_that("Carbon correction (csv, El-MAVEN export (with set names))", {
  resolution <- 140000
  resolution_defined_at <- 200
  input_file <- system.file(
    "extdata",
    "elmaven_export.csv",
    package = "accucor"
  )

  # This file includes the empty line from exported "set names" which is also
  # incorrectly formatted (one too few columns)
  # Warnings from parsing this input are expected
  corrected <- expect_warning(natural_abundance_correction(
    path = input_file,
    output_base = FALSE,
    resolution = resolution,
    resolution_defined_at = resolution_defined_at
  ))

  expected_output <- list(
    "Original" = read_expected(
      system.file(
        "extdata",
        "elmaven_export_corrected.xlsx",
        package = "accucor"
      ),
      sheet = 1
    ),
    "Corrected" = read_expected(
      system.file(
        "extdata",
        "elmaven_export_corrected.xlsx",
        package = "accucor"
      ),
      sheet = "Corrected"
    ),
    "Normalized" = read_expected(
      system.file(
        "extdata",
        "elmaven_export_corrected.xlsx",
        package = "accucor"
      ),
      sheet = "Normalized"
    ),
    "PoolAfterDF" = read_expected(
      system.file(
        "extdata",
        "elmaven_export_corrected.xlsx",
        package = "accucor"
      ),
      sheet = "PoolAfterDF"
    )
  )

  expect_equivalent(corrected, expected_output)
})


test_that("Carbon correction (Excel, El-MAVEN export (with set names))", {
  resolution <- 140000
  resolution_defined_at <- 200
  input_file <- system.file(
    "extdata",
    "elmaven_export.xlsx",
    package = "accucor"
  )

  corrected <- natural_abundance_correction(
    path = input_file,
    output_base = FALSE,
    resolution = resolution,
    resolution_defined_at = resolution_defined_at
  )

  expected_output <- list(
    "Original" = read_expected(
      system.file(
        "extdata",
        "elmaven_export_corrected.xlsx",
        package = "accucor"
      ),
      sheet = 1
    ),
    "Corrected" = read_expected(
      system.file(
        "extdata",
        "elmaven_export_corrected.xlsx",
        package = "accucor"
      ),
      sheet = "Corrected"
    ),
    "Normalized" = read_expected(
      system.file(
        "extdata",
        "elmaven_export_corrected.xlsx",
        package = "accucor"
      ),
      sheet = "Normalized"
    ),
    "PoolAfterDF" = read_expected(
      system.file(
        "extdata",
        "elmaven_export_corrected.xlsx",
        package = "accucor"
      ),
      sheet = "PoolAfterDF"
    )
  )

  expect_equal(corrected, expected_output)
})


test_that("Carbon correction (csv, El-MAVEN export (w/o names))", {
  resolution <- 140000
  input_file <- system.file(
    "extdata",
    "elmaven_d2_export.csv",
    package = "accucor"
  )

  corrected <- natural_abundance_correction(
    path = input_file,
    resolution = resolution,
    output_base = FALSE
  )

  expected_output <- list(
    "Original" = read_expected(
      system.file(
        "extdata",
        "elmaven_d2_export_corrected.xlsx",
        package = "accucor"
      ),
      sheet = 1
    ),
    "Corrected" = read_expected(
      system.file(
        "extdata",
        "elmaven_d2_export_corrected.xlsx",
        package = "accucor"
      ),
      sheet = "Corrected"
    ),
    "Normalized" = read_expected(
      system.file(
        "extdata",
        "elmaven_d2_export_corrected.xlsx",
        package = "accucor"
      ),
      sheet = "Normalized"
    ),
    "PoolAfterDF" = read_expected(
      system.file(
        "extdata",
        "elmaven_d2_export_corrected.xlsx",
        package = "accucor"
      ),
      sheet = "PoolAfterDF"
    )
  )

  expect_equal(corrected, expected_output)
})


test_that("Carbon correction (csv, El-MAVEN, multiple groups per compound)", {
  resolution <- 140000
  input_file <- system.file(
    "extdata",
    "alanine_three_peak_groups.csv",
    package = "accucor"
  )

  corrected <- natural_abundance_correction(
    path = input_file,
    resolution = resolution,
    output_base = FALSE
  )

  expected_output <- list(
    "Original" = read_expected(
      system.file(
        "extdata",
        "alanine_three_peak_groups_corrected.xlsx",
        package = "accucor"
      ),
      sheet = 1
    ),
    "Corrected" = read_expected(
      system.file(
        "extdata",
        "alanine_three_peak_groups_corrected.xlsx",
        package = "accucor"
      ),
      sheet = "Corrected"
    ),
    "Normalized" = read_expected(
      system.file(
        "extdata",
        "alanine_three_peak_groups_corrected.xlsx",
        package = "accucor"
      ),
      sheet = "Normalized"
    ),
    "PoolAfterDF" = read_expected(
      system.file(
        "extdata",
        "alanine_three_peak_groups_corrected.xlsx",
        package = "accucor"
      ),
      sheet = "PoolAfterDF"
    )
  )

  expect_equal(corrected, expected_output)
})

# Test using dataframe input/output
test_that("Carbon correction (dataframe)", {
  resolution <- 100000
  input_data <- as.data.frame(
    readxl::read_excel(
      path = system.file(
        "extdata",
        "C_Sample_Input_Simple.xlsx",
        package = "accucor"
      ),
      sheet = 1
    )
  )

  corrected <- natural_abundance_correction(
    data = input_data,
    resolution = resolution
  )

  expected_output <- list(
    "Original" = read_expected(
      system.file(
        "extdata",
        "C_Sample_Input_Simple.xlsx",
        package = "accucor"
      ),
      sheet = 1
    ),
    "Corrected" = read_expected(
      system.file(
        "extdata",
        "C_Sample_Input_Simple_corrected.xlsx",
        package = "accucor"
      ),
      sheet = "Corrected"
    ),
    "Normalized" = read_expected(
      system.file(
        "extdata",
        "C_Sample_Input_Simple_corrected.xlsx",
        package = "accucor"
      ),
      sheet = "Normalized"
    ),
    "PoolAfterDF" = read_expected(
      system.file(
        "extdata",
        "C_Sample_Input_Simple_corrected.xlsx",
        package = "accucor"
      ),
      sheet = "PoolAfterDF"
    )
  )
  expect_equal(corrected, expected_output)
})


# Test using newer El-Maven export with added columns
test_that("Carbon correction (El-Maven v0.11.0)", {
  resolution <- 100000
  input_file <- system.file(
    "extdata",
    "elmaven_v0.11_export.csv",
    package = "accucor"
  )

  corrected <- natural_abundance_correction(
    path = input_file,
    resolution = resolution,
    output_base = FALSE
  )

  expected_output <- list(
    "Original" = read_expected(
      system.file(
        "extdata",
        "elmaven_v0.11_export_corrected.xlsx",
        package = "accucor"
      ),
      sheet = 1
    ),
    "Corrected" = read_expected(
      system.file(
        "extdata",
        "elmaven_v0.11_export_corrected.xlsx",
        package = "accucor"
      ),
      sheet = "Corrected"
    ),
    "Normalized" = read_expected(
      system.file(
        "extdata",
        "elmaven_v0.11_export_corrected.xlsx",
        package = "accucor"
      ),
      sheet = "Normalized"
    ),
    "PoolAfterDF" = read_expected(
      system.file(
        "extdata",
        "elmaven_v0.11_export_corrected.xlsx",
        package = "accucor"
      ),
      sheet = "PoolAfterDF"
    )
  )
  expect_equal(corrected, expected_output)
})